MPDZ p.Val1447=
c.4341A>G · rs61753784 · VCV211514
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 11.4%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.18 | GERP -2.7, phastCons 0.004 |
| Overall | ||
| CADD | 5.898 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
11.4%
African / African-American · 8,538/74,860 alleles
Filtering AF
11.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 11.1%
Overall
0.624%
10,070/1,613,018 alleles · common
exomes 5,115/1,460,876 · genomes 4,955/152,142 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 11.4% | 9 |
| Remaining individualsnot grpmax-eligible | 0.908% | 110 |
| Admixed American | 0.869% | 115 |
| Middle Eastern | 0.693% | 144 |
| South Asian | 0.0352% | 2,843 |
| European (non-Finnish) | 0.0312% | 3,205 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,560 |
| Finnishnot grpmax-eligible | 0.00156% | 63,962 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- MPDZ
- Protein
- p.Val1447=
- Coding
- c.4341A>G
- MANE Select
- NM_001378778
- dbSNP
- rs61753784
- Type
- single nucleotide variant
- Location
- chr9:13136134 (GRCh38)
- Structure
- AlphaFold pLDDT 72.11 · 3 PDB
Similar variants
- MPDZ p.Val1447Leu Uncertain significance ★ same residue
- MPDZ c.1087-1G>A Pathogenic/Likely pathogenic ★★ same type
- MPDZ c.1474+2T>C Likely pathogenic ★★ same type
- MPDZ c.3359+1G>A Likely pathogenic ★★ same type
- MPDZ c.3360-2A>G Pathogenic/Likely pathogenic ★★ same type
- MPDZ c.4003+1G>A Pathogenic/Likely pathogenic ★★ same type
- MPDZ p.Arg1034Ter Pathogenic/Likely pathogenic ★★ same type
- MPDZ p.Arg1071Ter Pathogenic ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/mpdz-p-val1447 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown